Can I use ICE to analyze CRISPR Knock-ins?

You can find an invitation to try the "beta" version of our ICE knock-in analysis tool here.

Since ICE KI Analysis is designed to work with Sanger data, it is most useful for analyzing knock-ins that fall within the practical range of Sanger sequencing. Synthego recommends an upper limit of 200nt insertions, including the homology arms aligned with this insert.

This makes ICE perfect for looking at gene tagging knock-ins, which typically fall within this range. The tool can also be used to analyze SNV edits. It should be noted, however, that due to the limits of Sanger sequencing, results for these very small knock-ins will have a larger margin of error, sometimes overestimating the prevalence of SNV edits, and underestimating Wild Type in the sample population. Stringent adherence to proper PCR protocols can help ensure the maximum possible accuracy when generating Sanger data for use with ICE.

Try running a few of your own knock-in samples through the tool, or take a look at our own example data. And please, don’t forget to leave your comments on our online Feedback Form.

If you have any questions, please contact support@synthego.com. We will be happy to contact you via email for a follow-up conversation.